title: Highly efficient quencher-free molecular beacon systems containing 2-ethynyldibenzofuran- and 2-ethynyldibenzothiophene-labeled 2'-deoxyuridine units.
abstract: We have prepared two fluorescent DNA probes--UDBF and UDBT, containing 2-ethynyldibenzofuran and 2-ethynyldibenzothiophene moieties, respectively, covalently attached to the base dU--and incorporated them in the central positions of oligodeoxynucleotides (ODNs) so as to develop new types of quencher-free linear beacon probes and investigate the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. The ODNs containing adenine flanking bases (FBs) displayed a selective fluorescence "turn-off" response to mismatched targets with guanine bases; this suggests that these probes could be used as base-discriminating fluorescent nucleotides. On the other hand, we observed a "turn-on" response to matched targets when the UDBF and UDBT units of ODNs containing pyrimidine-based FBs were positioned opposite the four natural nucleobases. In particular, an ODN incorporating UDBT and cytosine FBs has potential use in single-nucleotide polymorphism typing.
authors.affiliation: Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, South Korea.
authors.forename: Jiwon
authors.initials: J
authors.lastname: Lee
authors.forename: Hyun Yi
authors.initials: HY
authors.lastname: Cho
authors.forename: Gil Tae
authors.initials: GT
authors.lastname: Hwang
mesh_terms: D020137:Base Pair Mismatch; D001572:Benzofurans / Q000737:chemistry*; D002942:Circular Dichroism; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism*; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry*; D004579:Electron Transport; D005456:Fluorescent Dyes / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence; D013876:Thiophenes / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D001572:Benzofurans; D015342:DNA Probes; D005456:Fluorescent Dyes; D009838:Oligodeoxyribonucleotides; D013876:Thiophenes; D003857:Deoxyuridine
keywords: DNA; electron transfer; fluorescent probes; oligonucleotides; single-nucleotide polymorphism